Creating and comprehending the circuitry of life: precise biomolecular design of multi-centre redox enzymes for a synthetic metabolism

创建和理解生命回路：用于合成代谢的多中心氧化还原酶的精确生物分子设计

• 批准号: BB/W003449/1
• 负责人: Ross Anderson
• 金额: $ 499.44万
• 依托单位: University of Bristol
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2022
• 资助国家: 英国
• 起止时间: 2022 至 无数据
• 项目状态: 未结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FW003449%2F1
• 关键词: Creating; comprehending; circuitry; life; precise

A defining characteristic of life is the requirement of energy from an external source; we eat, plants absorb light. To maximize the energy gained from the food that we and all oxygen-breathing organisms consume, oxygen is converted to water as a final step and carbon dioxide is released. The oxygen in this equation arises from plants as they convert water, carbon dioxide and light, into oxygen and fuel. This cycle is not merely an auspicious result of billions of years of evolution. The molecular events that allow the processes of respiration and photosynthesis to happen are connected in deep ways, down to shared structures, molecules, and mechanisms.At their most basic, respiration and photosynthesis are Nature's way to capture and convert energy from one form to another. To do this, Nature has evolved complex structures, termed oxidoreductases, that bind molecules that aid in this conversion. These molecules can both absorb light, imparting plants with their colours, and take and give electrons. The oxidoreductases have evolved to take energy from external sources and convert it into forms that can be used by living organisms to grow and survive. The evident complexity of this process belies a central feature of the oxidoreductases involved: evolution has yielded structures that are built from repeats of relatively simple modules. All of respiration and photosynthesis are built on these repeating modules. But despite nearly a century of investigation, where we have outlined how respiration and photosynthesis work in fine detail, we remain unable to construct our own models of these processes. This naturally leads to a question of whether we really understand how these processes occur. Here we have assembled a team of researchers from multiple academic institutions and disciplines to address deficiencies in our knowledge, with the unified target of building completely new oxidoreductases from scratch. Through this work we will fill holes in our understanding of how Nature captures and converts energy. Our work begins by combining powerful computational techniques that allow us to design and construct oxidoreductases with tailor made functions. Within a virtual reality framework that we are developing for this project, we will work together in a shared digital space to construct molecular binding sites, alter how molecules take and give electrons or catalyse reactions, and create oxidoreductase modules that, taking inspiration from Nature, we will join to produce more complex functions. With these designs, we will use an iterative 'build-test-learn' approach to construct new oxidoreductases that match the activities and actions of those Nature uses in respiration and photosynthesis. By pulling together our expertise in computational biophysical methods, oxidoreductase engineering, modular structure creation, molecular binding site assembly and their chemistry, and the analysis of very fast oxidoreductase functions, our team stands to make a substantial leap in our understanding of how to construct new oxidoreductases that has, so far, remained beyond our grasp. The principles we establish through this work will help us to better understand the oxidoreductases of respiration and photosynthesis, finally clarifying architectural features that are essential for their assembly and function that have remained opaque for over a century. With our new sets of design principles, we will be able to create oxidoreductases that fulfil our needs in bioscience and biotechnology, from the creation of single structures that produce fuels from light, water and carbon dioxide akin to photosynthesis to biosensors that detect toxins in the environment or signs of disease.

生命的定义特征是外部来源的能量要求。我们吃饭，植物吸收光。为了最大程度地利用我们和所有氧气呼吸生物消耗的食物所获得的能量，将氧气转化为水作为最后一步，并释放二氧化碳。该方程式中的氧气是由植物转化为氧气，二氧化碳和光的植物，变成氧气和燃料。这个周期不仅是数十亿年进化的吉祥结果。允许呼吸和光合作用过程发生的分子事件以深度的方式连接到共享结构，分子和机制。在其最基本，呼吸和光合作用的情况下，自然是捕获和转化能量从一种形式到另一种形式的方法。为此，自然已经发展出复杂的结构，这些结构称为氧化还原酶，这些结构结合了有助于这种转化的分子。这些分子都可以吸收光线，并赋予植物颜色，并拿出电子。氧化还原酶已经演变为从外部来源中获取能量，并将其转化为可以由活生物体生长和生存的形式。该过程的明显复杂性掩盖了所涉及的氧化还原酶的主要特征：进化产生了从相对简单模块的重复序列中构建的结构。所有呼吸和光合作用都建立在这些重复模块上。但是，尽管经过了近一个世纪的调查，但我们概述了呼吸和光合作用如何详细效果，但我们仍然无法构建自己的这些过程模型。这自然会导致一个问题，即我们是否真正了解这些过程是如何发生的。在这里，我们召集了来自多个学术机构和学科的研究人员团队，以解决我们所知的缺陷，其统一目标是从头开始建立全新的氧化还原酶。通过这项工作，我们将填补对自然如何捕捉和转化能量的理解的洞。我们的工作始于结合强大的计算技术，使我们能够使用量身定制的功能设计和构建氧化还原酶。在我们为该项目开发的虚拟现实框架中，我们将在共享的数字空间中共同努力，以构建分子结合位点，改变分子的采用方式并给予电子或催化反应，并创建氧化还原酶模块，从而从自然中获取灵感，我们将加入以产生更复杂的功能。通过这些设计，我们将使用迭代的“构建测试 - 学习”方法来构建新的氧化还原酶，以符合呼吸和光合作用中这些性质用途的活动和动作。通过将我们在计算生物物理方法，氧化还原酶工程，模块化结构创造，分子结合位点组装及其化学方面的专业知识中汇总在一起，以及对非常快速的氧化氧化还原酶功能的分析，我们的团队将实现实质性的飞跃，以实现我们对如何构建远距离构建新的氧化还原酶的理解。我们通过这项工作确定的原理将有助于我们更好地了解呼吸和光合作用的氧化还原酶，最后阐明对其组装和功能至关重要的建筑特征，这些特征在一个多世纪以来一直不透明。有了我们的新设计原理，我们将能够创建满足生物科学和生物技术需求的氧化酶，从创建单个结构的创建，这些结构产生来自光，水和二氧化碳的燃料，类似于光合作用到光合作用到生物传感器到在环境中检测毒素或疾病迹象的生物传感器。

项目成果

Fluctuation Relations to Calculate Protein Redox Potentials from Molecular Dynamics Simulations.

• DOI: 10.1021/acs.jctc.3c00785
• 发表时间: 2024-01-09
• 期刊: JOURNAL OF CHEMICAL THEORY AND COMPUTATION
• 影响因子: 5.5
• 作者: Oliveira, A. S. F.;Rubio, J.;Noble, C. E. M.;Anderson, J. L. R.;Anders, J.;Mulholland, A. J.
• 通讯作者: Mulholland, A. J.

Cellular production of a de novo membrane cytochrome.

• DOI: 10.1073/pnas.2300137120
• 发表时间: 2023-04-18
• 期刊: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
• 影响因子: 11.1
• 作者: Hardy, Benjamin J.;Hermosilla, Alvaro Martin;Chinthapalli, Dinesh K.;V. Robinson, Carol;Anderson, J. L. Ross;Curnow, Paul
• 通讯作者: Curnow, Paul

Heme binding to the SARS-CoV-2 spike glycoprotein.

• DOI: 10.1016/j.jbc.2023.105014
• 发表时间: 2023-08
• 期刊: JOURNAL OF BIOLOGICAL CHEMISTRY
• 影响因子: 4.8
• 作者: Freeman, Samuel L.;Oliveira, A. Sofia F.;Gallio, Andrea E.;Rosa, Annachiara;Simitakou, Maria K.;Arthur, Christopher J.;Mulholland, Adrian J.;Cherepanov, Peter;Raven, Emma L.
• 通讯作者: Raven, Emma L.